Yes, have had two gsd's with anal gland issues. The first one sounds like yours, kept treating infection which wouldn't go away. Finally the glands were removed surgically because the infection cause perianal fistula's. With that, my advice is, if the infection can't be cleared up completely, I would highly consider removing the glands (by a board certified surgeon who is experienced in this area).

I hope your vet shaved up the area as well, and advised you to keep it clean.

No idea what the bumps could be, hope they can figure that out. Hope he feels better, anal gland issues can be quite uncomfortable as well as painful